Development of a rapid low cost fluorescent biosensor for the detection of food contaminants

A prototype fluorescent based biosensor has been developed for the antibody based detection of food related contaminants. Its performance was characterised and showed a typical antibody binding signal of 200-2000 mV, a short term noise of 9.1 mV, and baseline slope of -0.016 mV/s over 4 h. Bulk signal detection repeatability (n=23) and reproducibility (n=3) were less than 2.4%CV. The biosensor detection unit was evaluated using two food related model systems proving its ability to monitor both binding using commercial products and inhibition through the development of an assay. This assay development potential was evaluated by observing the biosensor's performance whilst appraising several labelled antibody and glass slide configurations. The molecular interaction between biotin and an anti-biotin antibody was shown to be inhibited by 41% due to the presence of biotin in a sample. A food toxin (domoic acid) calibration curve was produced, with %CVs ranging from 2.7 to 7.8%, and a midpoint of approximately 17 ng/ml with further optimisation possible. The ultimate aim of this study was to demonstrate the working principles of this innovative biosensor as a potential portable tool with the opportunity of interchangeable assays. The biosensor design is applicable for the requirements of routine food contaminant analysis, with respect to performance, functionality and cost. (C) 2012 Elsevier B.V. All rights reserved.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

The not-so-extreme white dwarf of the CV GD 552

GD 552 is a cataclysmic binary which was previously believed to be composed of an M-star and a white dwarf, the latter having an extreme mass of 1.4 solar masses. In a recent paper we showed that this is not compatible with new observational evidence and presented an alternative model in which the white dwarf has a typical mass and the companion is a brown dwarf, making the system a likely member of the elusive group of CVs which have already evolved through minimum orbital period. Here we present additional spectroscopical evidence supporting this conclusion by means of skew mapping.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Production of a broad specificity antibody for the development and validation of an optical SPR screening method for free and intracellular microcystins and nodularin in cyanobacteria cultures

A highly sensitive broad specificity monoclonal antibody was produced and characterised for microcystin detection through the development of a rapid surface plasmon resonance (SPR) optical biosensor based immunoassay. The antibody displayed the following cross-reactivity: MC-LR 100%; MC-RR 108%; MC-YR 68%; MC-LA 69%; MC-LW 71%; MC-LF 68%; and Nodularin 94%. Microcystin-LR was covalently attached to a CM5 chip and with the monoclonal antibody was employed in a competitive 4min injection assay to detect total microcystins in water samples below the WHO recommended limit (1µg/L). A 'total microcystin' level was determined by measuring free and intracellular concentrations in cyanobacterial culture samples as this toxin is an endotoxin. Glass bead beating was used to lyse the cells as a rapid extraction procedure. This method was validated according to European Commission Decision 96/23/EC criteria. The method was proven to measure intracellular microcystin levels, the main source of the toxin, which often goes undetected by other analytical procedures and is advantageous in that it can be used for the monitoring of blooms to provide an early warning of toxicity. It was shown to be repeatable and reproducible, with recoveries from spiked samples ranging from 74 to 123%, and had % CVs below 10% for intra-assay analysis and 15% for inter-assay analysis. The detection capability of the assay was calculated as 0.5ng/mL for extracellular toxins and 0.05ng/mL for intracellular microcystins. A comparison of the SPR method with LC-MS/MS was achieved by testing six Microcystis aeruginosa cultures and this study yielded a correlation R(2) value of 0.9989.

Estimating male and female height inequality

This study investigates the coefficient of variation (CV) of height of males and females as a measure of inequality. We have collected a data set on corresponding male and female height CVs from 124 populations, spanning the period between the 1840s and 1980s. The results suggest that the R2 between the two CVs is 0.39, with the male CV being greater, indicating higher plasticity.

Anthropometric within-country Inequality and the Estimation of Skill Premia with Anthropometric Indicators

Recently, a method to measure inequality has been proposed that is based on an- thropometric indicators. Baten (1999, 2000) argued that the coefficient of variation of human stature (henceforth ‘CV’) is correlated with overall inequality in a society, and that it can be used as indicator, especially where income inequality measures are lack- ing. This correlation has been confirmed in further analyses, for example by Pradhan et al. (2003), Moradi and Baten (2005), Sunder (2003), Guntupalli and Baten (2006), Blum (2010a), van Zanden et al. (2010), see also Figure 1 and Table 1. The idea is that average height reflects nutritional conditions during early childhood and youth. Since wealthier people have better access to food, shelter and medical resources, they tend to be taller than the poorer part of the population. Hence, the variation of height of a cer- tain cohort may be indicative of income distribution during the decade of their birth. The aim of this study is firstly to provide an overview of different forms of within- country height inequality. Previous studies on the aspects of height inequality are re- viewed. Inequalities between ethnic groups, gender, inhabitants of different regions and income groups are discussed. In the two final sections, we compare height CVs of anthropological inequality with another indicator of inequality, namely skill premia. We also present estimates of skill premia for a set of countries and decades for which “height CVs”, as they will be called in the following, are available.

Roche tomography of cataclysmic variables - VI. Differential rotation of AE Aqr - not tidally locked!

We present Roche tomograms of the K4V secondary star in the cataclysmic variable AE Aqr, reconstructed from two data sets taken 9 d apart, and measure the differential rotation of the stellar surface. The tomograms show many large, cool starspots, including a large high-latitude spot and a prominent appendage down the trailing hemisphere. We find two distinct bands of spots around 22° and 43° latitude, and estimate a spot coverage of 15.4-17 per cent on the Northern hemisphere. Assuming a solar-like differential rotation law, the differential rotation of AE Aqr was measured using two different techniques. The first method yields an equator-pole lap time of 269 d and the second yields a lap time of 262 d. This shows that the star is not fully tidally locked, as was previously assumed for CVs, but has a co-rotation latitude of ˜40°. We discuss the implications that these observations have on stellar dynamo theory, as well as the impact that spot traversal across the L1 point may have on accretion rates in CVs as well as some of their other observed properties. The entropy landscape technique was applied to determine the system parameters of AE Aqr. For the two independent data sets, we find M1 = 1.20 and 1.17 M⊙, M2 = 0.81 and 0.78 M⊙, and orbital inclinations of 50° to 51° at optimal systemic velocities of γ = -64.7 and -62.9 km s-1.

Deep Eutectic Solvents Based on N-Methylacetamide and a Lithium Salt as Electrolytes at Elevated Temperature for Activated Carbon-Based Supercapacitors

The impact of accretion disc winds on the optical spectra of cataclysmic variables

Many high-state non-magnetic cataclysmic variables (CVs) exhibit blueshifted absorption or P-Cygni profiles associated with ultraviolet (UV) resonance lines. These features imply the existence of powerful accretion disc winds in CVs. Here, we use our Monte Carlo ionization and radiative transfer code to investigate whether disc wind models that produce realistic UV line profiles are also likely to generate observationally significant recombination line and continuum emission in the optical waveband. We also test whether outflows may be responsible for the single-peaked emission line profiles often seen in high-state CVs and for the weakness of the Balmer absorption edge (relative to simple models of optically thick accretion discs). We find that a standard disc wind model that is successful in reproducing the UV spectra of CVs also leaves a noticeable imprint on the optical spectrum, particularly for systems viewed at high inclination. The strongest optical wind-formed recombination lines are H alpha and He ii lambda 4686. We demonstrate that a higher density outflow model produces all the expected H and He lines and produces a recombination continuum that can fill in the Balmer jump at high inclinations. This model displays reasonable verisimilitude with the optical spectrum of RW Trianguli. No single-peaked emission is seen, although we observe a narrowing of the double-peaked emission lines from the base of the wind. Finally, we show that even denser models can produce a single-peaked H alpha line. On the basis of our results, we suggest that winds can modify, and perhaps even dominate, the line and continuum emission from CVs.

Detection of MegaTAL-induced HIV pol Mutation By Droplet Digital PCR

Thesis (Master's)--University of Washington, 2015

Chirality in the new generation of antidepressants: stereoselective analysis of the enantiomers of mirtazapine, N-demethylmirtazapine, and 8-hydroxymirtazapine by LC-MS.

Mirtazapine is an antidepressant that acts specifically on noradrenergic and sertonergic receptors. A LC-MS method was developed that allows the simultaneous analysis of the R-(-)- and S-(+)-enantiomers of mirtazapine (MIR), demethylmirtazapine (DMIR), and 8-hydroxymirtazapine (8-OH-MIR) in plasma of MIR-treated patients. The method involves a 3-step liquid-liquid extraction, an HPLC separation on a Chirobiotic V column, and MS detection in electrospray mode. The limit of quantification (LOQ) for all enantiomers was 0.5 ng/mL, and the intra- and interday CVs were within 3.3% to 11.7% (concentration ranges 5-50 ng/mL). A method is also presented for the quantitative analysis of glucuroconjugated MIR and 8-OH-MIR. S-(+)-8-OH-MIR is present in plasma mainly as its glucuronide. Preliminary data suggest that in all patients, except in those comedicated with CYP2D6 inhibitors such as fluoxetine and thioridazine, R-(-)-MIR concentrations were higher than those of S-(+)MIR. Moreover, fluvoxamine seems also to inhibit the metabolism of MIR. Therefore, this method seems to be suitable for the stereoselective assay of MIR and its metabolites in plasma of patients comedicated with MIR and other drugs for routine and research purposes.

Facteurs de risque de calcifications vasculaires en insuffisance rénale constituant une contre-indication à la greffe rénale

On estime que des calcifications vasculaires (CVs) sont présentes chez 60% des patients avec insuffisance rénale terminale (IRT) et que ces CVs contribuent à l’augmentation de la maladie cardiovasculaire chez ces patients. La maladie cardiovasculaire est la première cause de mortalité chez les patients en IRT. La transplantation rénale est le traitement de choix en IRT mais peut être contre-indiquée pour des raisons chirurgicales liées au CVs ou en raison d’un risque de complications cardiovasculaires postopératoires trop élevé associé à la présence de CVs sévères. Il est donc primordial de déterminer quels facteurs sont associés à la présence de CVs qui rendraient le patient non-éligible pour une greffe rénale. En particulier il serait intéressant de vérifier si un produit phosphocalcique élevé est un facteur de risque de non-éligibilité pour une greffe rénale en raison de CVs. L’étude actuelle utilise la base de données de transplantation du CHUM. C’est une étude de type cas-témoins avec une cohorte de 1472 patients de 1992 à 2009. Les cas sont les patients jugés non-éligibles pour une transplantation rénale en raison de la présence de CVs sévères. Les contrôles sont les patients jugés éligibles: 80 cas et 80 contrôles ont été inclus. Les facteurs de risque qui ont été identifiés pour la non-éligibilité en raison de CVs sont le diabète (adjusted Odds Ratio (OR): 5.55 (1.98 - 15.59)), l’âge (OR: 1.14 (1.09 – 1.2)), le tabagisme (OR: 9.51 (2.55 – 35.51)) et la dialyse (OR: 6.83 (2.33 – 20.05)). La durée de la dialyse a aussi été identifiée comme facteur de risque (OR : 8.61 (2.34-31.68) pour une durée de dialyse de 8 mois et plus, OR : 4.57 (1.42-14.65) pour une durée de dialyse de 1 à 7 mois. Bien que significatif en univarié, le produit phosphocalcique n’a pas été identifié comme facteur de risque significatif dans les analyses multivariées. En conclusion, cette étude montre que le produit phosphocalcique pourrait être un marqueur d’une insuffisance rénale prolongée et moins bien contrôlée plutôt qu’un facteur de risque de calcifications rendant le patient non-éligible à la greffe. De plus cette étude met de l’emphase sur la notion qu’il est primordial 1) de référer précocement les patients à haut risque de CVs vers un centre de transplantation pour une évaluation et 2) de prendre en charge agressivement l’arrêt du tabac chez tous les patients qui sont potentiellement éligibles pour une transplantation.

A Study of Coir Vyvasaya Co-Operative Societies in Kerala – Performance, Problems and Prospects

The present study was undertaken to evaluate the performance of Coir Vyavasaya Co-operative societies (CVCs) in Kerala. It was also intended to examine the extent of fulfillment of the objectives of Co-operativisation Scheme and the socio-economic betterment of worker members, Further the study was directed to find out the level of participation of members in the affairs of CVCs and to identify the major problems confronting the CVCs and the future prospects of the industry. The objectives of this study are to evaluate the performance of CVCs in Kerala with reference to the objectives of co-operativisation, socio-economic background of the worker members of the CVCs in the state, extent of members participation, major problems etc. Major findings of the study shows that 84% of CVCs surveyed were incurring losses, the long-term solvency position of the CVCS shows very pathetic situation, ration analysis shows and unhealthy state of affaires with respect to short-term solvency position and operating efficiency of all categories of CVS were found to be extremely poor. If CVCs are enabled to increase their quantity of production and there by the volume of business, their amount of loss can be reduced. If this is so, the societies can provide more days of employment to their work members, which will help them to earn more wages and thereby improve their economic and social conditions

CoObRA: Eine Plattform zur Verteilung und Replikation komplexer Objektstrukturen mit optimistischen Sperrkonzepten

In der vorliegenden Arbeit wird die Konzeption und Realisierung der Persistenz-, Verteilungs- und Versionierungsbibliothek CoObRA 2 vorgestellt. Es werden zunächst die Anforderungen an ein solches Rahmenwerk aufgenommen und vorhandene Technologien für dieses Anwendungsgebiet vorgestellt. Das in der neuen Bibliothek eingesetzte Verfahren setzt Änderungsprotokolle beziehungsweise -listen ein, um Persistenzdaten für Dokumente und Versionen zu definieren. Dieses Konzept wird dabei durch eine Abbildung auf Kontrukte aus der Graphentheorie gestützt, um die Semantik von Modell, Änderungen und deren Anwendung zu definieren. Bei der Umsetzung werden insbesondere das Design der Bibliothek und die Entscheidungen, die zu der gewählten Softwarearchitektur führten, eingehend erläutert. Dies ist zentraler Aspekt der Arbeit, da die Flexibilität des Rahmenwerks eine wichtige Anforderung darstellt. Abschließend werden die Einsatzmöglichkeiten an konkreten Beispielanwendungen erläutert und bereits gemachte Erfahrungen beim Einsatz in CASE-Tools, Forschungsanwendungen und Echtzeit-Simulationsumgebungen präsentiert.